1/ Deep-time phylogenetics is hard: overly simplistic substitution models can mislead tree estimation at the billion year timescale. Our new preprint introduces GTRspmix, a protein modeling framework designed to more realistically model site-to-site heterogeneity in amino acid replacement. 🧵

1/ Our new paper in Systematic Biology "Modeling Site-and-Branch-Heterogeneity with GFmix" led by @cgpmcc.bsky.social describes improved ways to model compositional heterogeneity across both sites and branches—an important source of error in deep phylogenomics. doi.org/10.1093/sysb...

Modeling Site-and-Branch-Heterogeneity with GFmix

Abstract. Phylogenetic trees are often inferred from protein sequences sampled from diverse taxa across the tree of life. The compositions of these amino a

doi.org

Have you registered for CGUE yet? Head on over to comparativegenomics2026.com Registration includes all meals and hotel nights.

IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models academic.oup.com/mbe/article/...

IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models

Abstract. IQ-TREE (https://iqtree.github.io/) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelih

academic.oup.com

#Archaea, #DPANN, #phylogenetic_reconciliation New preprint online! www.biorxiv.org/content/10.1...

Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages

The phylogeny of the Archaea continues to be revisited and revised as new groups are discovered and phylogenetic methods improve, but key questions about their early evolution remain. It has been sugg...

biorxiv.org

Pleased to share our new preprint: "Plasmodium ARK1 regulates spindle formation during atypical mitosis and forms a divergent chromosomal passenger complex". Many thanks to our collaborators. @ritatewari.bsky.social @eelcotromer.bsky.social @davidguttery.bsky.social www.biorxiv.org/content/10.1...

Our paper describing our new improved GFmix models for phylogenetic inference that capture site-and-branch heterogeneity in amino acid composition. www.biorxiv.org/content/10.1...

Modeling site-and-branch-heterogeneity with GFmix

Phylogenetic trees are often inferred from protein sequences sampled from diverse taxa across the tree of life. The compositions of these amino acid sequences may be heterogeneous across both sites an...

biorxiv.org

Modeling site-and-branch-heterogeneity with GFmix https://www.biorxiv.org/content/10.1101/2025.08.07.669136v1

Phylogenetic dissection provides insights into the incongruity in the tree of Archaeplastida between the analyses of nucleus- and plastid-encoded proteins. https://www.biorxiv.org/content/10.1101/2025.05.06.652364v1

Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data | mBio journals.asm.org/doi/10.1128/...

Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data | mBio

Advancements in next-generation sequencing have made whole-genome shotgun (WGS) metagenomic sequencing an efficient method for de novo reconstruction of microbial genomes from various environments. Th...

journals.asm.org

New paper out! We discovered a tiny archaeon with the smallest known archaeal genome — only 238 kbp! Candidatus Sukunaarchaeum mirabile has almost no recognizable metabolic pathways and may rely heavily on a host to survive. It also represents a novel, deep-branching lineage in the archaeal tree.

bioRxiv Evolutionary Biology@biorxiv-evobio.bsky.social · last yr.

A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome https://www.biorxiv.org/content/10.1101/2025.05.02.651781v1

A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome https://www.biorxiv.org/content/10.1101/2025.05.02.651781v1